ASP error "./stereo.default could not be found"

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Yu Lu

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Jul 11, 2020, 10:33:20 AM7/11/20
to Ames Stereo Pipeline Support
Ubuntu: 18.04
ISIS: 3.9.1
python: 3.7.6
ASP: 2.6.2 / 2.7.2

Hi guys,

When I used ASP to generate CTX DEM, a warning below occured, can anyone tell me how to solve this problem?

Warning: Stereo file: ./stereo.default could not be found. Will use default settings and command line options only.

cheers,
Yu

Yu Lu

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Jul 11, 2020, 10:37:11 AM7/11/20
to Ames Stereo Pipeline Support
here is the log file.
Yu


在 2020年7月11日星期六 UTC+8下午10:33:20，Yu Lu写道：
out-log-stereo_fltr-07-11-2218-22125.txt

Michael Walpert

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Jul 11, 2020, 11:22:18 AM7/11/20
to Yu Lu, Ames Stereo Pipeline Support
ASP is expecting to find a file called Stereo.default in the directory where you're trying to run your operation.

The Stereo.default file contains a bunch of options that can be modified for various operations.

You should be able to find it in your root directory for ASP. If it's not there, you should also have a  copy located in your "*\ASP\examples\K10" folder

Copy it and paste it into the directory where you're running your stereo operation.

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Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]

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Jul 11, 2020, 3:45:56 PM7/11/20
to Michael Walpert, Yu Lu, Ames Stereo Pipeline Support
Yeah, that is a warning, not an error. It just says that if that file is missing it won't be used. All the options in stereo.default can be set on the command line by pre-pending them with two dashes.


From: ames-stereo-pi...@googlegroups.com <ames-stereo-pi...@googlegroups.com> on behalf of Michael Walpert <mlwa...@gmail.com>
Sent: Saturday, July 11, 2020 8:22 AM
To: Yu Lu <grds...@gmail.com>
Cc: Ames Stereo Pipeline Support <ames-stereo-pi...@googlegroups.com>
Subject: [EXTERNAL] Re: ASP error "./stereo.default could not be found"
 
Message has been deleted

Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]

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Jul 12, 2020, 2:54:45 PM7/12/20
to Yu Lu, Ames Stereo Pipeline Support
This is an ISIS error. You need to fetch ISIS data, likely the "base" and "mro" data, and set ISISROOT. See our documentation for more details. 
From: ames-stereo-pi...@googlegroups.com <ames-stereo-pi...@googlegroups.com> on behalf of Yu Lu <grds...@gmail.com>
Sent: Sunday, July 12, 2020 8:59 AM
To: Ames Stereo Pipeline Support <ames-stereo-pi...@googlegroups.com>
Subject: Re: [EXTERNAL] Re: ASP error "./stereo.default could not be found"
 
Dear Michael and Alexandrov,

Thanks for your reply. I copied the stereo.default file and pasted it to the directory where I run ASP, but errors occurred:

(isis3) pmo@pmo-xps:~/data/CTX/new$ stereo g19_025728_1693_xn_10s328w_cal.map.cub d09_030897_1692_xn_10s328w_cal.map.cub results/out

[ 2020-Jul-12 23:54:41 ] : Stage 0 --> PREPROCESSING 
        --> Setting number of processing threads to: 8
Writing log info to: results/out-log-stereo_pprc-07-12-2354-6224.txt
Using session: isis.
Loading camera model: g19_025728_1693_xn_10s328w_cal.map.cub 
Using image files:  g19_025728_1693_xn_10s328w_cal.map.cub, d09_030897_1692_xn_10s328w_cal.map.cub
Using "./stereo.default"
        --> Computing statistics for left
          left: [ lo:0.0323661 hi:0.121755 m: 0.0754739 s: 0.0144903]
        --> Computing statistics for right
          right: [ lo:0.064752 hi:0.138569 m: 0.0914303 s: 0.0105644]
        --> Normalizing globally to: [0.0323661 0.138569]
Loading camera model: g19_025728_1693_xn_10s328w_cal.map.cub 


Error: **ERROR** Unable to initialize camera model from group [Instrument].
**PROGRAMMER ERROR** Unable to create a shape model from given target and pvl.
**I/O ERROR** Invalid shape model file [$base/dems/molaMarsPlanetaryRadius0005.cub] in Kernels group.
**ERROR** The given shape model file is not a valid ISIS DEM. Unable to open as an ISIS cube.
**I/O ERROR** Unable to open [$ISISDATA/base/dems/molaMarsPlanetaryRadius0005.cub].
**ERROR** The given shape model file is not a valid NAIF DSK file. Unable to construct a NAIF DSK shape model.
**USER ERROR** NAIF DSK file [$base/dems/molaMarsPlanetaryRadius0005.cub] does not exist.
Stereo step 0: Preprocessing failed

What's wrong?
Cheers,
Yu
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Yu Lu

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Jul 13, 2020, 5:30:20 AM7/13/20
to Ames Stereo Pipeline Support
Hi Oleg,

I have fetched "base" and "mro" data already (but no kernels). I tried to set ISISROOT like this:

export ISISROOT=/home/pmo/software/anaconda3/envs/isis3 (I installed ISIS3 with anaconda)

source $ISISROOT/scripts/isis3Startup.sh

However, the errors still existed. 

I'm not familiar with the linux or ASP. I don't know why it still dosen't work. 

I would appreciate if you could give me some detailed advice. Thanks.

Yu

Beyer, Ross A. (ARC-SST)[SETI INSTITUTE]

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Jul 13, 2020, 11:09:15 AM7/13/20
to Yu Lu, Ames Stereo Pipeline Support
Yu,

I can imagine how little familiarity with linux would make all of this seem difficult to decipher.

Sounds like you have installed ISIS via anaconda. From a fresh terminal window, after you “activate” your isis conda environment, can you run the following commands and paste their output:

> cat $CONDA_PREFIX/version

> cat $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

> echo $ISISROOT

> echo $ISIS3DATA


The error you are getting:
**USER ERROR** NAIF DSK file [$base/dems/molaMarsPlanetaryRadius0005.cub] does not exist.

Is complaining about a file that should be located at $ISIS3DATA/base/dems/molaMarsPlanetaryRadius0005.cub

When you are in an active ISIS conda environment, you should be able to

> cd $ISIS3DATA/base/dems/
> ls

And see what files are in that directory.

Do you have that file?




> On Jul 13, 2020, at 2:30 AM, Yu Lu <grds...@gmail.com> wrote:
>
> Hi Oleg,
>
> I have fetched "base" and "mro" data already (but no kernels). I tried to set ISISROOT like this:
>
> export ISISROOT=/home/pmo/software/anaconda3/envs/isis3 (I installed ISIS3 with anaconda)
>
> source $ISISROOT/scripts/isis3Startup.sh
>
> However, the errors still existed.
>
> I'm not familiar with the linux or ASP. I don't know why it still dosen't work.
>
> I would appreciate if you could give me some detailed advice. Thanks.
>
> Yu
>
>
> 在 2020年7月13日星期一 UTC+8上午2:54:45，Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]写道：
> This is an ISIS error. You need to fetch ISIS data, likely the "base" and "mro" data, and set ISISROOT. See our documentation for more details.
> From: ames-stereo-pi...@googlegroups.com <ames-stereo-pi...@googlegroups.com> on behalf of Michael Walpert <mlwa...@gmail.com>
> Sent: Saturday, July 11, 2020 8:22 AM
> To: Yu Lu <grds...@gmail.com>
> Cc: Ames Stereo Pipeline Support <ames-stereo-pi...@googlegroups.com>
> Subject: [EXTERNAL] Re: ASP error "./stereo.default could not be found"
>
> ASP is expecting to find a file called Stereo.default in the directory where you're trying to run your operation.
>
> The Stereo.default file contains a bunch of options that can be modified for various operations.
>
> You should be able to find it in your root directory for ASP. If it's not there, you should also have a copy located in your "*\ASP\examples\K10" folder
>
> Copy it and paste it into the directory where you're running your stereo operation.
>
> On Sat, Jul 11, 2020 at 9:37 AM Yu Lu <grds...@gmail.com> wrote:
> here is the log file.
> Yu
>
>
> 在 2020年7月11日星期六 UTC+8下午10:33:20，Yu Lu写道：
> Ubuntu: 18.04
> ISIS: 3.9.1
> python: 3.7.6
> ASP: 2.6.2 / 2.7.2
>
> Hi guys,
>
> When I used ASP to generate CTX DEM, a warning below occured, can anyone tell me how to solve this problem?
>
> Warning: Stereo file: ./stereo.default could not be found. Will use default settings and command line options only.
>
> cheers,
> Yu
>
> --
> You received this message because you are subscribed to the Google Groups "Ames Stereo Pipeline Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ames-stereo-pipeline...@googlegroups.com.
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>
> --
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>
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>
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Ross

http://RossBeyer.net/science/

Yu Lu

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Jul 13, 2020, 11:08:16 PM7/13/20
to Ames Stereo Pipeline Support
Hi Ross,

Thanks for your reply.

Yeah. It is not easy for me to do these things. I have run the commands you said in the terminal:

(base) pmo@pmo-xps:~$ source activate isis3
(isis3) pmo@pmo-xps:~$ cat $CONDA_PREFIX/version
3.9.1 # Public version number
2019-11-19 # Release date
stable # Release stage (alpha, beta, stable)
(isis3) pmo@pmo-xps:~$ cat $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
#!/bin/sh
export ISISROOT=/home/pmo/software/anaconda3/envs/isis3
export ISIS3DATA=/home/pmo/software/anaconda3/envs/isis3/data
export ISIS3TESTDATA=/home/pmo/software/anaconda3/envs/isis3/testData
(isis3) pmo@pmo-xps:~$ echo $ISISROOT
/home/pmo/software/anaconda3/envs/isis3
(isis3) pmo@pmo-xps:~$ echo $ISIS3DATA
/home/pmo/software/anaconda3/envs/isis3/data
(isis3) pmo@pmo-xps:~$ 

When the error occurred, I have checked "molaMarsPlanetaryRadius0005.cub" in the directory, and it is there. That's why I'm confused. Please see attached picture.7@~%C%)PBN4ZK~82~I7Z(]T.png

Cheers,
Yu
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Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]

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Jul 14, 2020, 12:28:16 AM7/14/20
to Yu Lu, Ames Stereo Pipeline Support
Ah. I see that you are setting

export ISIS3DATA=/home/pmo/software/anaconda3/envs/isis3/data

but it is complaining:

> **I/O ERROR** Unable to open [$ISISDATA/base/dems/molaMarsPlanetaryRadius0005.cub]. 

So you should set ISISDATA, not ISIS3DATA, if you are using the latest ASP which is 2.7.0 with conda. 

I know this is terribly confusing. The ISIS folks recently switched to ISISDATA instead of ISIS3DATA.

In short, if your ASP version is less than 2.7.0 and your ISIS version is less than 4.0 then you should use ISIS3DATA. Else, it is suggested you use the latest ASP 2.7.0 fetchable with conda or from our daily build (https://byss.arc.nasa.gov/stereopipeline/daily_build/) together with ISIS 4.1.0 and then set ISISDATA.

Sorry. See if it works or if something else is wrong.

Oleg



Sent: Monday, July 13, 2020 8:08 PM
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Yu Lu

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Jul 15, 2020, 10:09:41 AM7/15/20
to Ames Stereo Pipeline Support
Hi Oleg,

Thanks for your advice. I used ASP 2.6.2 and set ISIS3DATA. It worked.

I selected two stereo CTX images in PILOT website (https://pilot.wr.usgs.gov/). The convergence angle of the images are around 20 degrees. I processed them with following comands:

mroctx2isis

spiceinit

ctxcal

cam2map4stereo.py

stereo

point2dem

However, there are many blanks in the output dem. Please see attached figure. I have tried several groups of images, and got the same problem. I'm wondering if the images I selected are not suitable? 

fig.png


Thanks for your time.

Best wishes,
Yu

Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]

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Jul 15, 2020, 12:34:33 PM7/15/20
to Yu Lu, Ames Stereo Pipeline Support
I am glad things worked.

I don't work with CTX much. I know some pairs have problems with illumination. Ideally the left and right image should be acquired very close in time. 

Maybe other folks will have better ideas. Here's one pair which works reasonably well:

J03_045994_1986_XN_18N282W
J03_046060_1986_XN_18N282W

Note that ISIS provides a way of cropping a cub to make the process faster, with their crop command, which can help with experimentation. Our stereo_gui can help with determining the crop window.

Sent: Wednesday, July 15, 2020 7:09 AM
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Michael Walpert

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Jul 15, 2020, 12:42:49 PM7/15/20
to Ames Stereo Pipeline Support
That DEM looks a lot like some of what I've seen from a couple images I processed. I'm pretty sure those voids are caused by shadows. It looks like you have higher elevation just to the south, so those shadows are interfering with  the generation.

You can use the --dem-hole-fill-len tag to interpolate and fill in those voids. Units for the tag are in pixels. Just be aware that you're essentially guessing at what the camera can't directly see.

Ex: point2dem [Image1.cub] [Image2.cub] --dem-hole-fill-len 20

Yu Lu

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Jul 16, 2020, 9:40:29 AM7/16/20
to Ames Stereo Pipeline Support
Dear Walpert,

Thanks for your advice. I'm wondering what [image1.cub], [Image2.cub] you said refer to. I have tried like this:

point2dem output-PC.tif --dem-hole-fill-len 20

But it seems that nothing has happened, the voids still exist.

Cheers,
Yu

在 2020年7月16日星期四 UTC+8上午12:42:49，Michael Walpert写道：

Alexandrov, Oleg (ARC-TI)[KBR Wyle Services, LLC]

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Jul 16, 2020, 12:35:53 PM7/16/20
to Yu Lu, Ames Stereo Pipeline Support
You can try a bigger value for --dem-hole-fill-len. And before that, you can compare no --dem-hole-fill-len versus having it in to see if there is any difference. That will show what size of holes get filled, if anything at all.

Once the DEM is created one can also use dem_mosaic with the --hole-fill-length option to fill holes. 

Illumination and shadow problems are big deal for stereo. It may be worth trying to find a different CTX pair for that area, or a HiRISE pair (if that aligns with your work). 
Sent: Thursday, July 16, 2020 6:40 AM
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